Contacts of the helix formed by residues 189 - 201 (chain F) in PDB entry 4NFI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 189 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186F VAL 3.7 20.6 - - - +
187F ARG 3.0 6.9 + - - +
188F PHE* 1.3 76.2 - - - +
190F GLU* 1.3 60.1 + - - +
191F LYS* 3.7 8.1 + - - +
192F ARG* 3.0 25.6 + - - +
193F TYR* 2.9 29.1 + - - +
267F CYS* 4.5 0.5 - - - -
272F VAL* 4.1 4.7 - - - -
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Residues in contact with GLU 190 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F THR* 1.3 73.0 - - - +
191F LYS* 1.3 63.9 + - - +
193F TYR* 3.3 6.5 + - + +
194F LYS* 2.9 53.6 + - + +
272F VAL* 3.7 14.6 - - + +
273F GLN* 4.6 7.4 + - - +
276F GLN* 3.0 31.3 + - - +
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Residues in contact with LYS 191 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F THR* 3.3 7.9 + - - +
190F GLU* 1.3 78.5 - - - +
192F ARG* 1.3 65.0 + - - +
194F LYS* 3.3 16.2 + - - +
195F SER* 3.1 21.9 + - - +
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Residues in contact with ARG 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F LEU* 3.9 30.1 + - - +
176F LEU* 4.5 12.7 - - - +
177F THR* 2.9 33.5 + - + +
187F ARG 3.9 16.6 - - - +
189F THR* 3.0 19.4 + - - +
191F LYS* 1.3 82.0 - - - +
193F TYR* 1.3 65.4 + - - +
195F SER* 3.2 10.2 + - - -
196F ILE* 3.0 36.7 + - + +
267F CYS* 4.7 1.8 - - - -
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Residues in contact with TYR 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189F THR 2.9 17.1 + - - +
190F GLU* 3.5 8.7 - - + +
192F ARG* 1.3 77.5 - - - +
194F LYS* 1.3 73.0 + - + +
196F ILE* 3.2 6.2 + - + +
197F VAL* 3.1 53.3 + - + +
237F GLU* 5.1 1.3 - - + -
240F GLN 3.6 0.3 - - - -
241F ILE* 3.4 44.3 + - + +
244F ASP* 2.7 30.1 + - - -
267F CYS* 3.1 30.7 - - - -
268F SER 3.9 2.7 - - - -
269F TRP* 3.3 27.5 - + + +
272F VAL* 4.0 13.5 - - + -
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Residues in contact with LYS 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190F GLU* 2.9 45.2 + - + +
191F LYS* 3.8 7.9 - - - +
192F ARG 3.2 0.2 - - - -
193F TYR* 1.3 81.5 - - + +
195F SER* 1.3 58.3 + - - +
197F VAL* 3.5 8.7 - - - +
198F LYS* 3.0 32.3 + - - +
234F GLU* 5.8 2.0 - - - -
237F GLU* 3.3 38.7 + - - +
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Residues in contact with SER 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173F LEU* 4.1 14.0 - - - +
191F LYS* 3.1 15.4 + - - +
192F ARG* 3.4 16.1 - - - -
194F LYS* 1.3 76.4 - - - +
196F ILE* 1.3 67.6 + - - +
198F LYS* 3.5 5.5 + - - -
199F TYR* 3.3 32.9 + - - +
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Residues in contact with ILE 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170F GLY* 4.1 2.7 - - - +
173F LEU* 3.8 26.9 - - + +
174F ASP* 4.1 19.3 - - + +
177F THR* 3.8 22.2 - - - +
192F ARG* 3.0 29.6 + - + +
193F TYR* 3.2 6.7 + - + +
195F SER* 1.3 77.5 - - - +
197F VAL* 1.3 62.1 + - + +
199F TYR* 3.8 1.4 - - - +
200F LYS* 2.8 53.1 + - + +
267F CYS* 4.0 31.0 - - + +
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Residues in contact with VAL 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193F TYR* 3.1 44.7 + - + +
194F LYS* 3.5 11.2 - - - +
196F ILE* 1.3 76.5 - - + +
198F LYS* 1.3 69.7 + - - +
200F LYS* 4.1 12.3 - - - -
201F THR* 3.0 19.9 + - - -
202F ALA* 3.0 10.1 + - - +
236F GLY 5.2 0.5 - - - +
237F GLU* 4.0 33.4 - - + -
240F GLN* 3.4 34.8 - - + -
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Residues in contact with LYS 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194F LYS 3.0 20.4 + - - +
195F SER* 3.7 8.7 - - - +
197F VAL* 1.3 81.4 - - - +
199F TYR* 1.3 84.9 + - + +
202F ALA* 3.3 23.5 + - + +
203F PHE* 3.3 37.9 - - + -
233F LEU* 4.6 20.5 - - + +
237F GLU* 6.1 1.3 - - - +
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Residues in contact with TYR 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165F TYR* 6.4 1.3 - + - -
166F GLN* 3.2 29.9 - - + +
167F THR* 3.2 21.5 + - - -
169F ILE* 4.1 18.2 - - + -
170F GLY* 3.4 19.7 - - - +
173F LEU* 4.9 7.0 - - + -
195F SER* 3.3 22.7 + - - +
197F VAL 3.3 0.2 - - - -
198F LYS* 1.3 111.3 + - + +
200F LYS* 1.3 64.6 + - - +
201F THR 3.4 0.9 + - - -
203F PHE* 3.9 23.3 - + - +
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Residues in contact with LYS 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167F THR* 3.4 10.9 - - - +
170F GLY* 3.7 22.2 - - - -
171F GLN* 3.8 5.2 - - - +
174F ASP* 2.9 31.2 + - + +
196F ILE* 2.8 35.7 + - + +
197F VAL* 4.1 5.8 - - - -
199F TYR* 1.3 74.4 - - - +
201F THR* 1.3 63.9 + - - +
204F TYR* 3.4 8.1 - - - -
240F GLN* 3.7 29.6 - - - +
244F ASP* 4.9 2.4 + - - -
266F LYS* 5.8 0.2 - - - +
401F JD5 2.6 67.0 + - + +
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Residues in contact with THR 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60F ARG* 5.7 0.4 - - - +
197F VAL 3.0 9.1 + - - -
199F TYR 3.3 0.6 - - - -
200F LYS* 1.3 83.4 - - - +
202F ALA* 1.3 69.0 + - - +
203F PHE 3.4 2.0 + - - -
204F TYR* 3.6 6.7 + - + -
205F SER* 3.1 32.5 + - - +
206F PHE* 5.1 0.2 - - + -
236F GLY 4.2 5.4 - - - +
239F PHE* 3.8 27.1 - - + -
240F GLN* 2.7 39.1 + - + +
401F JD5 3.0 21.1 + - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il